It is possible to hide any other folders on the terminal server user's C drive so that the only folders they see are the shared folders they have access to? It isn't a huge issue but I think it would be cleaner and easier if they users only saw the folders they could access. Something like Hidden share
There's ABE (access based enumeration) but I'm not sure it's appropriate in this scenario.
http://technet.microsoft.com/en-us/library/cc784710(WS.10).aspx
Without knowing anything about your use case I don't know if this is applicable to you but you could create the folder tree within each user's personal profile. Other users then shouldn't see them because they won't have access to that profile.